Novel genomes can be analyzed by the program GeneMark-ES utilizing unsupervised training.
Note that GeneMark-ES has a special mode for analyzing fungal genomes.
Recently, we have developed a semi-supervised version of GeneMark-ES, called GeneMark-ET that uses RNA-Seq reads to improve training.
For several species pre-trained model parameters are ready and available through the GeneMark.hmm page.

Gene Prediction in Transcripts

Sets of assembled eukaryotic transcripts can be analyzed by the modified GeneMarkS algorithm
(the set should be large enough to permit self-training).
A single transcript can be analyzed by a special version of GeneMark.hmm with Heuristic models.
A new advanced algorithm GeneMarkS-T was developed recently (manuscript sent to publisher);
The GeneMarkS-T software (beta version) is available for
download .